Compositions and Methods for Treating Huntington&#39;s Disease and Related Disorders

ABSTRACT

Compositions and methods are provided for the inhibition, treatment and/or prevention of Huntington&#39;s disease and related disorders.

This application is a continuation of U.S. patent application Ser. No.15/766,549, filed on Apr. 6, 2018, which is a § 371 application ofPCT/US2016/056417, filed Oct. 11, 2016, which claims priority under 35U.S.C. § 119(e) to U.S. Provisional Patent Application No. 62/352,788,filed Jun. 21, 2016 and U.S. Provisional Patent Application No.62/239,714, filed Oct. 9, 2015. The foregoing applications areincorporated by reference herein.

Incorporated herein by reference in its entirety is the Sequence Listingbeing concurrently submitted via EFS-Web as a XML file named SeqList,created Mar. 6, 2023, and having a size of 587,341 bytes.

This invention was made with government support under grant numberNS084475 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to polyglutamine (polyQ) disorders,particularly Huntington's disease. Specifically, the instant inventionprovides compositions and methods for the treatment and/or prevention ofHuntington's disease and related disorders.

BACKGROUND OF THE INVENTION

Huntington disease (HD) is an autosomal dominant neurodegenerativedisease that manifest in adults (adult-onset HD) or children (JuvenileHD). HD is part of the family of polyglutamine (polyQ) disorderscomprising at least nine different neurodegenerative diseases thatresult from the expansion of a triplet CAG repeat in specific genes(Walker, F. O. (2007) Lancet, 369:218-228). In HD, the disease causingmutation is found in the first exon of the huntingtin gene, and althoughmutant huntingtin is ubiquitously expressed, the brain, and particularlythe striatum and motor cortex are the earliest and most affected(Walker, F. O. (2007) Lancet, 369:218-228; The Huntington's DiseaseCollaborative Research Group (1993) Cell, 72, 971-983). Patients with HDdevelop progressive neurodegeneration leading to death, generally within20 years of onset.

There is no cure for HD, and treatments are focused on managing itssymptoms (Johnson et al. (2010) Hum. Mol. Genet., 19:R98-R102). Earlierstudies using genetically modified mouse models showed that HD-likedisease phenotypes can be resolved if mutant huntingtin expression iseliminated, even at advanced disease stages (Yamamoto et al. (2000)Cell, 101:57-66; Diaz-Hernandez et al. (2005) J. Neurosci.,25:9773-9781). RNA interference (RNAi), a method of reducing geneexpression, has emerged as a leading therapeutic option. RNAi does noteliminate all mutant huntingtin, however, and therefore it remainsexpressed at low levels. For this reason, there is a need for effectivetherapeutics for HD.

SUMMARY OF THE INVENTION

In accordance with one aspect of the instant invention, methods andcompositions for inhibiting, treating, and/or preventing a polyglutaminedisorder (e.g., Huntington's disease) in a subject are provided. Inaccordance with another aspect of the instant invention, methods forreducing the expression of a mutant protein (e.g., mutant huntingtin)encoded by an allele of a gene associated with a polyglutamine disorder(e.g., Huntington's disease) in a cell are provided. In a particularembodiment, the methods of the instant invention comprise administeringto the subject or cell a nucleic acid molecule encoding Cas9 and atleast one guide RNA (e.g., sgRNA). In a particular embodiment, the guideRNA are administered to the subject or cell as a nucleic acid molecule(e.g., an expression vector or viral vector) encoding the guide RNA. Ina particular embodiment, the methods of the instant invention compriseadministering two guide RNAs to the subject or cell. In a particularembodiment, one guide RNA targets a sequence 5′ of exon 1 (e.g., withinthe 5′ untranslated region, within the promoter, or within the first 2kb 5′ of the transcription start site) and one guide RNA targets asequence within intron 1. In a particular embodiment, at least one guideRNA administered to the subject or cell targets a sequence adjacent to aPAM present on only one allele of the gene (e.g., the mutant allele). Ina particular embodiment, at least one of the guide RNAs targets asequence specifically set forth herein.

The instant invention also encompasses guide RNAs, nucleic acidmolecules (e.g., an expression vector or viral vector) encoding theguide RNAs, and compositions comprising the guide RNAs and/or nucleicacid molecules (e.g., an expression vector or viral vector) encoding theguide RNAs. In a particular embodiment, the composition and nucleic acidmolecules (e.g., an expression vector or viral vector) encoding theguide RNAs contain or encode more than one guide RNA.

BRIEF DESCRIPTIONS OF THE DRAWING

FIG. 1A provides a schematic depicting the genomic deletion mechanism bythe sgRNA/Cas9 complex. FIG. 1B shows the targeting sequences of the HTTpromoter (top) and PCR results demonstrating genomic deletion intranfected cells (bottom). FIG. 1C provides a schematic depictinggenomic deletion mechanism by sgRNA/Cas9 complex (left) and strategyadopted to achieve allele specific gene editing based on location ofsingle nucleotide polymorphisms at the third nucleotide sequence of thePAM motif (right).

FIG. 2A provides a schematic of the targeting of Cas9 to allele specificPAM motifs by sgRNA. The loss of a PAM (left), gain of a PAM (center),and a loss/gain (right) are depicted. FIG. 2B provides examples ofallele specific PAM motifs based on Streptococcus pyogenes (SpCas9;PAM—NRG) and Staphylococcus aureus Cas9 (SaCas9; PAM—NNGRR, NNGRRT). Thenucleotide variation of a SNP within a PAM alters Cas9 recognitionresulting in the loss (Left), the gain (Middle), or the simultaneousloss of a PAM in one DNA strand and the gain of a PAM on the oppositestrand (Right). FIG. 2C shows the locations of examples (Table 1) of theSNP ID's and genomic localization of the nucleotide variants targeted bySpCas9/sgRNA complex in the promoter and first intron sequence of thehuman huntingtin genomic locus.

FIGS. 3A-3C: SNP dependent editing for Huntington disease therapy. FIG.3A: Cartoon depicting the allele specific editing strategy to abrogatemutant HTT expression. SNPs within PAM sequences upstream of HTT exon1permit specific targeted deletions of the mutant allele when present inheterozygosity. After DNA repair mutant HTT exon1 is deleted by a pairof sgRNA/Cas9 complexes binding upstream and downstream of exon1(Right), whereas intronic indels could be generated by a single dsDNAbreak in the normal allele (Left). FIG. 3B provides a schematic of anormal allele and a mutant allele in the presence of sgHD1 and sgHDi3.The presence of both sgRNAs causes the cleavage of only the mutantallele. FIG. 3C: 21 out of 47 prevalent SNPs flanking HTT exon1 arelocated within predicted critical positions of a PAM sequence for theCRISPR/SpCas9 system analyzed. The minor frequency allele eithermediates the loss (8 SNPs), again (8 SNPs) or a loss/gain (5 SNPs) of aPAM motif. FIGS. 3D-3J: List of the 36 prevalent SNPsupstream/downstream of HTT exon1 that fall within the nucleotidepositions of the different CRISPR/Cas9 and CRISPR/Cpf1 systems analyzed.Sequences in FIG. 3D are SEQ ID NOs: 74-120, from top to bottom. FIG. 3Kshows the flanking sequence of the indicated SNPs, the location of thePAMs, and an example of complementary sequence to target the site forcleavage. Nucleotide variations at specific genomic DNA sequencesresults in the loss or the loss/gain of SNP-dependent PAM motifs whichgenerate or eliminate the recruitment of SpCas9/sgRNA to the huntingtingenomic locus. SEQ ID NOs are provided in parentheses.

FIGS. 4A-4I: Cleavage of SNP-dependent sgHD/SpCas9 complexes in HEK293cells. FIG. 4A: Cartoon depicting the relative position of the 6prevalent SNP-dependent PAMs upstream of HTT exon1, and 2 common PAMswithin HTT intron 1. The estimated size of the targeted deleted sequenceis indicated. FIG. 4B: Genotype of the prevalent SNPs within the HTTpromoter in HEK293 cells. All SNPs were homozygous for the nucleotidevariation and the PAM motif was present for the sgRNA indicated. FIG.4C: Diagram of the CRISPR expression systems transfected into HEK293cells. FIGS. 4D-4F: Genomic PCR showing HTT exon1-targeted deletion bysgRNA/SpCas9 pair complexes binding upstream and downstream of thetarget sequence. FIG. 4G: RT-qPCR analysis of HTT mRNA levels in HEK293cells transfected with sgHD/SpCas9 expression cassettes targetingupstream promoter SNPs and the common intronic sgHDi3 sequence. Allsamples are normalized to human GAPDH and results are the mean±SEMrelative to cells transfected with plasmids containing the SpCas9 onlycontrol. (n=64P<0.001, #P<0.0001, One way ANOVA followed by aBonferroni's post-hoc). FIG. 4H: sgHD1/i3/SpCas9 and sgHD3/i3/SpCas9 andsgHDi3/SpCas9 expression cassettes were transfected into HEK293 cells,and endogenous HTT protein levels were determined after puromycinselection and expansion. Cells transfected with Cas9 only was used as acontrol and betacatenin served as a loading control. FIG. 4I:Quantification of HTT protein levels after treatment with sgHD/SpCas9complexes. Data are the mean±SEM relative to cells transfected withplasmids containing SpCas9 only control. (n=6; #P<0.0001, § P<0.001, oneway ANOVA followed by Bonferroni's post-hoc). FIG. 4J: Sanger sequencingof PCR amplified products after of HTT exon1 editing with sgHD/Cas9expression vectors targeting upstream promoter SNPs and the intronic i3PAM. SEQ ID NOs are provided in parentheses. FIG. 4K: RT-qPCR analysisof HTT mRNA levels in HEK293 cells transfected with sgHD/SpCas9expression cassettes targeting upstream promoter SNPs and commonintronic sgHDi4 sequences. All samples are normalized to human GAPDH andresults are mean±SEM relative to cells transfected with plasmidscontaining SpCas9 only control. (n=4). FIG. 4L provides a schematicdepicting the strategy to delete 1st exon sequence of mutant huntingtingene using the CRISPR/Cas9 system targeting the SNP-derived PAM motifsat positions SNP1, SNP2, SNP3 and SNP6 in combination with the intronici3 PAM motif (top). A representative experiment is also provided(bottom) showing deletion of HTT genomic fragment after coexpression ofSNP and i3 targeting CRISPR/Cas9 expression systems. Arrow indicatesexpected DNA bands derived from cleavage and NHEJ recombination. FIG. 4Mprovides a schematic depicting the strategy to delete 1st exon sequenceof mutant huntingtin gene using the CRISPR/Cas9 system targeting theSNP6 in combination with i3 PAM motif (top). A representative experimentis also provided (bottom) showing deletion of HTT genomic fragment aftercoexpression of SNP6 and i3 targeting CRISPR/Cas9 expression systems.Arrow indicates expected DNA bands derived from cleavage and NHEJrecombination using 3 different primer sets. FIG. 4N provides aschematic depicting the strategy to delete 1st exon sequence of mutanthuntingtin gene using the CRISPR/Cas9 system targeting the SNP4, SNP5derived PAM motifs in combination with i3 PAM motif (top).Representative experiments are provided (bottom) showing deletion of HTTgenomic fragment after coexpression of SNP targeting CRISPR/Cas9systems. Arrow indicates expected DNA bands derived from cleavage andNHEJ recombination.

FIGS. 5A-5O: List of SNP-dependent PAMs targeted by different CRISPRsystems. SEQ ID NOs are provided in parentheses.

FIGS. 6A-6B: List of sgRNA sequence designed for targeting prevalentSNP-dependent PAM motifs present upstream 5′ of HTT exon1, and commonsgHD sequences within HTT intron 1. SEQ ID NOs are provided inparentheses.

FIGS. 7A-7H: Assessment of allele specific cleavage in human HDfibroblasts. FIG. 7A: Cartoon depicting the CRISPR expression plasmiduse to co-express sgHD1 and sgHDi3 expression cassettes. SpCas9 and theselective reporter eGFP/puromycin expression cassettes present in thesame plasmid are also shown. FIG. 7B: ND31551 and ND33392 HD fibroblastslines were selected to determine allele specific target deletions ofHTT. CAG repeat length, nucleotide variation and the allele location ofthe PAM motif are indicated. FIG. 7C: Representative genomic PCR showingHTT exon1 deletion of DNA harvested from the electroporated ND31551 HDfibroblast cell line. Arrow indicates the expected PCR amplificationproduct resulting from allele specific deletion. FIGS. 7D and 7E:Semi-quantitative PCR reaction showing reduction of the targeted allelecontaining the conserved PAM sequence. For ND31551 fibroblasts the PAMsequence is conserved in the normal allele, while for ND33392fibroblasts the PAM sequence is in the mutant allele. Expression levelsare reduced only on the PAM-containing allele. FIG. 7F: Quantificationof mRNA reduction in treated HD fibroblasts. Data show the ratio betweenmRNA levels of the mutant with respect to the normal allele, relative tocells electroporated with vectors expressing only the Cas9 control. Theresults are mean±SEM relative to cells transfected with plasmidscontaining SpCas9 only control. (n=6; P<0.01, Mann Whitney T-test). FIG.7G: Representative western blot showing allele specific depletion (upperband of HTT doublet consisting of normal (lower) and expandedpolyQ-containing proteins) after electroporation of HD fibroblasts withsgHD/SpCas9 expression vectors. FIG. 7H: Western blot quantification ofHD fibroblasts electroporated with Cas9-hU6sgHD1/i3 expression vector.

FIGS. 8A-8D: Assessing off target activity of sgHD1 and sgHDi3/Cas9.FIG. 8A: Table depicting the number of off-target sites for the mostactive sequences predicted to bind with 1, 2 or 3 mismatches. Thenucleotide length of the complementary guide sequence is also indicated.FIG. 8B: Table highlighting the number of off-target sites binding atdifferent genomic regions using the UCSC genome browser. FIG. 8C: HDfibroblasts were electroporated with plasmids expressing sgHD1/i3 andSpCas9 along with an ODN sequence (SEQ ID NO: 417 and SEQ ID NO: 418(reverse complement)). Sanger sequencing results showed theincorporation of the ODN sequence at the DNA cleavage site. HTT promotersequence and HTT intron sequence outside the ODN sequence are alsodepicted (SEQ ID NOs: 419-424, from top to bottom). FIG. 8D: Sangersequencing results from 11 predicted off target sites. Gene name,chromosome position, DNA strand, number of mismatches and positionwithin the guide, gene location, sgRNA sequence and indel presence orabsence are indicated. Sequences are SEQ ID NOs: 425-435, from top tobottom.

FIGS. 9A-9C: In vivo gene editing of the mutant HTT allele. FIG. 9A:Cartoon depicting rAAV shuttle vectors containing the SpCas9 andsgHD1/i3 expression cassettes. mCMV, minimal CMV promoter; mpA, minimalpolyA. hU6p, human U6 promoter; pA, SV40 polyA. FIG. 9B: PCR of isolatedgenomic DNA showing human HTT exon1 targeted deletion after injection ofvectors expressing SpCas9 and sgRNA sequences. LStr, left Striatum;RStr, Right Striatum. FIG. 9C: RT-QPCR analysis of HTT mRNA levels instriatum samples harvested 3 weeks after SpCas9 and sgHD1/i3delivery.All samples were normalized to beta actin and results are mean±SEMrelative to uninjected striatal samples (n=7 animals per group, §P<0.001, Mann Whitney test). FIG. 9D: Genomic PCR products of DNAharvested after HTT exon1 editing in HEK 293 cells with rAAV2/1 SpCas9and rAAV2/1 vectors (Left) and representative western blot showingreduced human HTT protein levels in HEK293 cells after editing withrAAV2/1 SpCas9 and rAAV2/1 vectors (Right). FIG. 9E: RT-QPCR analysis ofmouse Htt mRNA levels in striatum samples harvested 3 weeks after rAAV.SpCas9 and rAAV.sgHDi3/1 injection. All samples were normalized to betaactin and results are mean±SEM relative to uninjected striatal samples(n=7 animals per group, § P<0.001, Mann Whitney test). Pairing betweensgHD1 and sgHDi3 to mouse HTT exon1 sequences is also shown. Oneoff-target site was identified for sgHDi3 in mouse Htt that contained 2mismatches. Three off-targets were identified in the case of sgHD1, allwith 5 mismatches between the mouse genomic sequence and the small guideRNA sequence. Sequences are SEQ ID NOs: 436-441, from top to bottom.

DETAILED DESCRIPTION OF THE INVENTION

Herein, therapeutics tools to inhibit mutant protein expression usinggenome-editing strategies based on the CRISPR/Cas9 technology areprovided. Targeted gene deletions can be introduced when guide RNAs(e.g., two guide RNAs) complex with Cas9 and mediate dsDNA breaksfollowed by DNA repair. Given the potency of the CRISPR/Cas9 technologyfor targeting both alleles, and the fact that huntingtin is an importantprotein for cell viability, a concern of this method is that one willeliminate all huntingtin in the cell—good and bad. Thus, approaches thatselectively target the expression of the mutant huntingtin allele aredesirable. Here, a gene editing approach for specific targeting of themutant huntingtin allele is provided. The strategy takes advantage ofsingle nucleotide polymorphisms prevalent in the population for which atargeting sequence (PAM motif) is generated depending on the nucleotidevariation. gRNA sequences have been developed that recruit CRISPR/Cas9complex to this allele-specific PAM motif. The safety and allelespecificity may be examined in vitro using human cell lines (e.g.,HEK293, NT2, HELA, neuronal precursor cell lines, HD fibroblasts (e.g.,derived from human patients) and in vivo with a new transgenic mouseexpressing the nucleotide variants within the HTT locus.

As explained above, the therapeutic benefit of RNA interference (RNAi)to reduce mutant huntingtin expression in different mouse models hasbeen shown (Harper et al. (2005) Proc. Natl. Acad. Sci., 102:5820-5825;Boudreau et al. (2009) Mol. Ther., 17:1053-1063; Drouet et al. (2009)Annals of Neurol., 65:276-285). However, RNAi treatment does notcompletely eliminate mutant huntingtin expression, and the mutantprotein remains present at low levels. This remaining protein maymitigate positive effects of RNAi therapy in HD patients. Thus, effortsto eliminate expression of all mutant HTT protein have been sought.Genome editing nucleases present such an opportunity.

Gene editing based on bacterial endonucleases such as CRISPR-associatedprotein-9 (Cas9) from Streptococcus pyogenes has revolutionized thefield (Cong et al. (2013) Science 339:819-823; Ran et al. (2013) NatureProtocols 8:2281-2308; Mali et al. (2013) Science 339:823-826; Jinek etal. (2012) Science 337:816-821). The RNA-guided CRISPR/Cas9 systeminvolves expressing Cas9 along with a guide RNA molecule (gRNA). Whencoexpressed, gRNAs bind and recruit Cas9 to a specific genomic targetsequence where it mediates a double strand DNA (dsDNA) break andactivates the dsDNA break repair machinery. Specific DNA fragments canbe deleted when two gRNA/Cas9 complexes generate dsDNA breaks atrelative proximity, and the genomic DNA (genDNA) is repaired bynonhomologous end joining (FIG. 1A). gRNAs were originally designed forrecruiting the CRISPR/Cas9 complex to the HTT promoter to deleteregulatory sequences and inhibit HTT expression (FIG. 1B). However, thecomplete elimination of the expression of both the normal and mutantalleles is likely not tolerable in human adults with HD. As such, anallele specific genome editing approach is provided herein where theCRISPR/Cas9 complex is targeted to the mutant HTT allele.

The binding specificity of the CRISPR/Cas9 complex depends on twodifferent elements. First, the binding complementarity between thetargeted genDNA sequence and the complementary recognition sequence ofthe gRNA. Second, the presence of a protospacer-adjacent motif (PAM)juxtaposed to the genDNA/gRNA complementary region. Whereas single pointmutations in the complementary recognition sequence permit Cas9-mediatedDNA cleavage, the preservation of an intact PAM motif is critical (Jineket al. (2012) Science 337:816-821; Hsu et al. (2013) Nat. Biotech.,31:827-832; Sternberg et al. (2014) Nature 507:62-67). The PAM motif forS. Pyogenes Cas9 has been fully characterized, and is NGG or NAG (Jineket al. (2012) Science 337:816-821; Hsu et al. (2013) Nat. Biotech.,31:827-832). While any nucleotide type can be found at the firstposition of the PAM motif, a C/T nucleotide at position 2 and/or a C/T/Anucleotide at position 3 can disrupt the PAM motif and subsequentlyinhibit Cas9-mediated dsDNA cleavage. Thus, PAM motifs containing singlenucleotide polymorphisms (SNP) at positions two or three will conferallele cleavage selectivity when targeted with CRISPR/Cas9 complexes.

The CAG (encoding glutamine) disease expansion in HTT is located withinthe 1^(st) exon of the HTT gene (The Huntington's Disease CollaborativeResearch Group (1993) Cell 72:971-983). A short exon 1 HTTpolyadenylated mRNA resulting from aberrant splicing of the mutantallele is reported to be translated into a pathogenic exon 1 HTT proteinand contribute to disease progression (Sathasivam et al. (2013) Proc.Natl. Acad. Sci., 110:2366-2370; Gipson et al. (2013) RNA Biol.,10:1647-1652). The main regulatory regions of the HTT promoter arelocated within the first 2 Kb upstream of the transcription start site(Holzmann et al. (2001) Brain Res., 92:85-97). The 1000 Genome databasehas reported the location and allele frequency of prevalent SNPs locatedin the promoter and within the first intronic sequence of the HTT gene(Abecasis et al. (2010) Nature 467:1061-1073). Table 1 provides selectedSNPs for allele-specific gene editing on the promoter of the HTT gene.Two examples of SNPs in the first intron of the HTT gene are rs28377140(3,079,906; G/C; + strand; gain/loss) and rs4498089 (3,080,199; A/G; +strand; gain.

TABLE 1 Prevalence of the targeted SNPs in the human huntingtin locus.From left to right the table information is: genomic location of the SNP(promoter, 5′UTR), variant ID (SNP identification), location (genomicposition), SNP (nucleotide variation), allele frequency based oninformation obtained from 1000 Genomes data base (Reference nucleotidevs variant nucleotide polymorphism), strand (positive or negativegenomic DNA strand), PAM (single nucleotide variation produces eitherthe loss or the loss/gain of a PAM motif at the opposite genomic DNAstrand). Allele frequency Location Variant ID Location SNP Reference1000G MAF Strand PAM Promoter rs35631490 3,071,679 C/G C = 0.8926 G =0.1074 + Loss Promoter rs61792464 3,073,385 G/C G = 0.8628 C = 0.1372 +Gain/Loss Promoter rs9996199 3,074,965 C/G C = 0.8425 G = 0.1575 +Gain/Loss Promoter rs2857935 3,075,691 C/G/T C = 0.7710 G = 0.2260 −Loss Promoter rs13122415 3,076,181 C/G C = 0.8918 G = 0.1082 + Loss5′UTR rs13102260 3,076,405 G/A G = 0.8419 A = 0.1581 + Loss

FIG. 2A provides a schematic of the targeting of Cas9 to allele specificPAM motifs by gRNA. The loss of a PAM (left), gain of a PAM (center),and a loss/gain (right) are depicted. FIG. 2B provides examples ofallele specific PAM motifs based on Streptococcus pyogenes (SpCas9;PAM—NRG) and Staphylococcus aureus Cas9 (SaCas9; PAM—NNGRR, NNGRRT; AnnRan et al. (2015) Nature 520:186-191). FIG. 2C shows the locations ofthe alleles listed in Table 1.

Clustered, regularly interspaced, short palindromic repeat (CRISPR)/Cas9technology is well known in the art (see, e.g., Sander et al. (2014)Nature Biotech., 32:347-355; Jinek et al. (2012) Science, 337:816-821).Cas9 possesses two nuclease domains, a RuvC-like nuclease domain and aHNH-like nuclease domain, and is responsible for the destruction of thetarget DNA (Jinek et al. (2012) Science, 337:816-821; Sapranauskas etal. (2011) Nucleic Acids Res. 39:9275-9282). The two nucleases generatedouble-stranded breaks. The double-stranded endonuclease activity ofCas9 requires a target sequence (e.g., ˜20 nucleotides) and a shortconserved sequence (˜2-5 nucleotides; e.g., 3 nucleotides) known asprotospacer-associated motif (PAM), which follows immediately 3′—of theCRISPR RNA (crRNA) complementary sequence (Jinek et al. (2012) Science,337:816-821; Nishimasu et al. (2014) Cell 156(5):935-49; Swarts et al.(2012) PLoS One, 7:e35888; Sternberg et al. (2014) Nature507(7490):62-7). Guidelines and computer-assisted methods for generatinggRNAs are available (see, e.g, CRISPR Design Tool (crispr.mit.edu/); Hsuet al. (2013) Nat. Biotechnol. 31:827-832; www.addgene.org/CRISPR; andCRISPR gRNA Design tool—DNA2.0 (www.dna20.com/eCommerce/startCas9)).Typically, the PAM sequence is present in the DNA target sequence butnot in the gRNA sequence.

As stated above, wild-type Cas9 creates a site-specific double-strandedDNA break. The double strand break can be repaired by non-homologous endjoining (NHEJ) pathway yielding an insertion and/or deletion or, in thepresence of a donor template, by homology-directed repair (HDR) pathwayfor replacement mutations (Overballe-Petersen et al. (2013) Proc. Natl.Acad. Sci. U.S.A. 110:19860-19865; Gong et al. (2005) Nat. Struct. Mol.Biol. 12:304-312). A Cas9 mutant may also be used in the instantinvention (e.g., a mutant with an inactivated HNH and/or RuvC nuclease).In a particular embodiment, the mutant is Cas9 D10A. Cas9 D10A nickssingle-strand DNA rather than generate a double strand break (Cong etal. (2013) Science, 339:819-823; Davis et al. (2014) Proc. Natl. Acad.Sci., 111:E924-932). The nicks are repaired by HDR pathway. Two gRNAscan be used to generate a staggered double strand break with Cas9 D10A.

In accordance with the instant invention, methods of treating,inhibiting, and/or preventing a polyglutamine disorder (e.g.,Huntington's disease) are provided. In accordance with another aspect ofthe instant invention, methods for reducing the expression of a mutantprotein (e.g., mutant huntingtin) encoded by an allele of a geneassociated with a polyglutamine disorder (e.g., Huntington's disease) ina cell are provided. Polyglutamine (polyQ) disorder are generallyneurodegenerative disorders which are caused by expandedcytosine-adenine-guanine (CAG) repeats (e.g., greater than about 36repeats) encoding a long polyQ tract in the respective proteins.Polyglutamine (polyQ) disorders include, without limitation,spinocerebellar ataxia (SCA; types 1, 2, 3, 6, 7, 17), Machado-Josephdisease (MJD/SCA3), Huntington's disease (HD), dentatorubralpallidoluysian atrophy (DRPLA), and spinal and bulbar muscular atrophy,X-linked 1 (SMAX1/SBMA). In a particular embodiment, the methods of theinstant invention comprise inhibiting, reducing, or eliminating mutantprotein (e.g., HTT) expression. In a particular embodiment, the methodcomprises inactivating (e.g., cleaving and/or deleting (at leastpartially (e.g., deleting the first exon))) mutant alleles (e.g., HTTalleles) using CRISPR/Cas9 technology. In a particular embodiment, themethod comprises administering at least one Cas9 (e.g., a nucleic acidmolecule encoding Cas9) and at least one gRNA (e.g., a nucleic acidmolecule encoding said gRNA) to said subject. Examples of Cas9 include,without limitation, Streptococcus pyogenes Cas9, Cas9 D10A, highfidelity Cas9 (Kleinstiver et al. (2016) Nature, 529:490-495; Slaymakeret al. (2016) Science, 351:84-88), Cas9 nickase (Ran et al. (2013) Cell,154:1380-1389), Streptococcus pyogenes Cas9 with altered PAMspecificities (e.g., SpCas9_VQR, SpCas9_EQR, and SpCas9_VRER;Kleinstiver et al. (2015) Nature, 523:481-485), Staphylococcus aureusCas9, the CRISPR/Cpf1 system of Acidaminococcus, and the CRISPR/Cpf1system of Lachnospiraceae. In a particular embodiment, the Cas9 is S.pyogenes Cas9. In a particular embodiment, the Cas9 has an inactivatedHNH and/or RuvC nuclease, particularly Cas9 D10A. In a particularembodiment, at least two gRNAs are delivered. In a particularembodiment, at least one gRNA targets a region adjacent to a PAM presentin only one allele (e.g., in the mutant allele). In a particularembodiment, the targeted PAM is in the 5′UTR, promoter, or first intron.In a particular embodiment, a second gRNA which is not targeted to theallele specific PAM is provided. In a particular embodiment, the secondgRNA targets anywhere from the 5′UTR to the 3′UTR of the gene (e.g., HTTgene), particularly within the first intron. In a particular embodiment,the method further comprises the administration of a donor nucleic acidmolecule (e.g., DNA; e.g., a nucleic acid molecule encoding the desiredsequence). The donor DNA may be a replacement sequence (e.g., wild-type)for the sequence excised from the mutant. The nucleic acids of theinstant invention may be administered consecutively (before or after)and/or at the same time (concurrently). The nucleic acid molecules maybe administered in the same composition or in separate compositions. Ina particular embodiment, the nucleic acid molecules are delivered in asingle vector (e.g., a viral vector).

The methods of the instant invention may also comprise theadministration of an additional therapeutic for Huntington's disease orthe related disorder. Other therapeutics include, without limitation:haloperidol, tetrabenazine, amantadine, huintingtin antisense,huntingtin siRNA, antidepressants, and antianxiety medications. Thenucleic acids of the instant invention and the other therapeutics may beadministered consecutively (before and/or after) and/or at the same time(concurrently). The other therapeutics may be administered in the samecomposition or in separate compositions as the nucleic acid molecules ofthe instant invention.

In a particular embodiment, the nucleic acid molecules of the instantinvention are delivered (e.g., via infection, transfection,electroporation, etc.) and expressed in cells via a vector (e.g., aplasmid), particularly a viral vector. The expression vectors of theinstant invention may employ a strong promoter, a constitutive promoter,and/or a regulated promoter. In a particular embodiment, the nucleicacid molecules are expressed transiently. Examples of promoters are wellknown in the art and include, but are not limited to, RNA polymerase IIpromoters, the T7 RNA polymerase promoter, and RNA polymerase IIIpromoters (e.g., U6 and H1; see, e.g., Myslinski et al. (2001) Nucl.Acids Res., 29:2502-09). Examples of expression vectors for expressingthe molecules of the invention include, without limitation, plasmids andviral vectors (e.g., adeno-associated viruses (AAVs), adenoviruses,retroviruses, and lentiviruses).

In a particular embodiment, the guide RNA of the instant invention maycomprise separate nucleic acid molecules. For example, one RNAspecifically hybridizes to a target sequence (crRNA) and another RNA(trans-activating crRNA (tracrRNA)) which specifically hybridizes withthe crRNA. In a particular embodiment, the guide RNA is a singlemolecule (sgRNA) which comprises a sequence which specificallyhybridizes with a target sequence (crRNA; complementary sequence) and asequence recognized by Cas9 (e.g., a tracrRNA sequence; scaffoldsequence). Examples of gRNA scaffold sequences are well known in the art(e.g., 5′-GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU AAGGCUAGUC CGUUAUCAACUUGAAAAAGU GGCACCGAGU CGGUGCUUUU; SEQ ID NO: 442). As used herein, theterm “specifically hybridizes” does not mean that the nucleic acidmolecule needs to be 100% complementary to the target sequence. Rather,the sequence may be at least 80%, 85%, 90%, 95%, 97%, 99%, or 100%complementary to the target sequences. The greater the complementarityreduces the likelihood of undesired cleavage events at other sites ofthe genome. In a particular embodiment, the region of complementarity(e.g., between a guide RNA and a target sequence) is at least about 10,at least about 12, at least about 15, at least about 17, at least about20, at least about 25, at least about 30, at least about 35, or morenucleotides. In a particular embodiment, the region of complementarity(e.g., between a guide RNA and a target sequence) is about 15 to about25 nucleotides, about 15 to about 23 nucleotides, about 16 to about 23nucleotides, about 17 to about 21 nucleotide, or about 20 nucleotides.In a particular embodiment, the guide RNA targets a sequence orcomprises a sequence (inclusive of RNA version of DNA molecules) as setforth in the Example or Figures provided herein (see, e.g., the guide ortarget sequences provided in FIGS. 5 and 6 ). In a particularembodiment, the guide RNA targets a sequence or comprises a sequencewhich has at least 80%, 85%, 90%, 95%, 97%, 99%, or 100% homology oridentity to a sequence set forth in the Examples and/or Figures (e.g.,FIGS. 5 and 6 ) provided herein. In a particular embodiment, the guideRNA targets a sequence selected from the group consisting of SEQ ID NOs:156-228 and 379-388. In a particular embodiment, the guide RNA comprisesa sequence selected from the group consisting of SEQ ID NOs: 156-228 and379-388 (e.g., in RNA form). The sequences may be extended or shortenedby 1, 2, 3, 4, or 5 nucleotides at the end of the sequence opposite fromthe PAM (i.e., the 5′ end). When the sequence is extended the addednucleotides should correspond to the HTT sequence. In a particularembodiment, one gRNA comprises sgHD1, sgHD2, sgHD3, sgHD4, sgHD5c,sgHD6c, or sgHD6g. In a particular embodiment, the second gRNA comprisessgHDi3 or sgHDi4. In a particular embodiment, one gRNA comprises sgHD1and one gRNA comprises sgHDi3.

As stated hereinabove, the instant invention provides nucleic acidmolecules, vectors, and compositions and methods for the inhibition,treatment, and/or prevention of Huntington's disease and relateddisorders. Compositions comprising at least one nucleic acid describedherein are also encompassed by the instant invention. In a particularembodiment, the composition comprises at least one, particularly atleast two, guide RNA (e.g., a nucleic acid molecule encoding the guideRNA (e.g., an expression vector)) and at least one pharmaceuticallyacceptable carrier. The composition may further comprise at least oneCas9 (e.g., a nucleic acid molecule encoding Cas9) and/or at least onedonor nucleic acid molecule. The composition may further comprise atleast one additional therapeutic (as described above). In a particularembodiment, all of the nucleic acid molecules are encoded within asingle expression vector (e.g., viral vector (e.g., AAV)).Alternatively, the other nucleic acid molecules may be contained withina separate composition(s) with at least one pharmaceutically acceptablecarrier. The present invention also encompasses kits comprising a firstcomposition comprising at least one guide RNA (e.g., a nucleic acidmolecule encoding the guide RNA (e.g., an expression vector)) and asecond composition comprising at least one Cas9 (e.g., a nucleic acidmolecule encoding Cas9) and/or at least one donor nucleic acid molecule.The first and second compositions may further comprise at least onepharmaceutically acceptable carrier. In a particular embodiment, thekits of the instant invention comprise a first composition comprising atleast one guide RNA (e.g., a nucleic acid molecule encoding the guideRNA (e.g., an expression vector)), at least one Cas9 (e.g., a nucleicacid molecule encoding Cas9), and/or at least one donor nucleic acidmolecule (optionally all within a single vector) and a secondcomposition comprising at least one additional therapeutic. The firstand second compositions may further comprise at least onepharmaceutically acceptable carrier.

As explained hereinabove, the compositions of the instant invention areuseful for treating Huntington's disease and related disorders. Atherapeutically effective amount of the composition may be administeredto a subject in need thereof. The dosages, methods, and times ofadministration are readily determinable by persons skilled in the art,given the teachings provided herein.

The components as described herein will generally be administered to apatient as a pharmaceutical preparation. The term “patient” or “subject”as used herein refers to human or animal subjects. The components of theinstant invention may be employed therapeutically, under the guidance ofa physician for the treatment of the indicated disease or disorder.

The pharmaceutical preparation comprising the components of theinvention may be conveniently formulated for administration with anacceptable medium (e.g., pharmaceutically acceptable carrier) such aswater, buffered saline, ethanol, polyol (for example, glycerol,propylene glycol, liquid polyethylene glycol and the like), dimethylsulfoxide (DMSO), oils, detergents, suspending agents or suitablemixtures thereof. The concentration of the agents in the chosen mediummay be varied and the medium may be chosen based on the desired route ofadministration of the pharmaceutical preparation. Except insofar as anyconventional media or agent is incompatible with the agents to beadministered, its use in the pharmaceutical preparation is contemplated.

Selection of a suitable pharmaceutical preparation depends upon themethod of administration chosen. For example, the components of theinvention may be administered by direct injection into any desiredtissue (e.g., brain) or into the surrounding area. In this instance, apharmaceutical preparation comprises the components dispersed in amedium that is compatible with blood or the target tissue.

The therapy may be, for example, administered parenterally, by injectioninto the blood stream (e.g., intravenous), or by subcutaneous,intramuscular or intraperitoneal injection. Pharmaceutical preparationsfor injection are known in the art. If injection is selected as a methodfor administering the therapy, steps must be taken to ensure thatsufficient amounts of the molecules reach their target cells to exert abiological effect.

Pharmaceutical compositions containing a compound of the presentinvention as the active ingredient in intimate admixture with apharmaceutical carrier can be prepared according to conventionalpharmaceutical compounding techniques. The carrier may take a widevariety of forms depending on the form of preparation desired foradministration, e.g., intravenous, oral or parenteral. In preparing theantibody in oral dosage form, any of the usual pharmaceutical media maybe employed, such as, for example, water, glycols, oils, alcohols,flavoring agents, preservatives, coloring agents and the like in thecase of oral liquid preparations (such as, for example, suspensions,elixirs and solutions); or carriers such as starches, sugars, diluents,granulating agents, lubricants, binders, disintegrating agents and thelike in the case of oral solid preparations (such as, for example,powders, capsules and tablets). Injectable suspensions may be prepared,in which case appropriate liquid carriers, suspending agents and thelike may be employed.

A pharmaceutical preparation of the invention may be formulated indosage unit form for ease of administration and uniformity of dosage.Dosage unit form, as used herein, refers to a physically discrete unitof the pharmaceutical preparation appropriate for the patient undergoingtreatment. Each dosage should contain a quantity of active ingredientcalculated to produce the desired effect in association with theselected pharmaceutical carrier. Procedures for determining theappropriate dosage unit are well known to those skilled in the art.Dosage units may be proportionately increased or decreased based on theweight of the patient. Appropriate concentrations for alleviation of aparticular pathological condition may be determined by dosageconcentration curve calculations, as known in the art.

The methods of the instant invention may further comprise monitoring thedisease or disorder in the subject after administration of thecomposition(s) of the instant invention to monitor the efficacy of themethod. For example, the subject may be monitored for characteristics ofHuntington's disease and related disorders.

Definitions

The singular forms “a,” “an,” and “the” include plural referents unlessthe context clearly dictates otherwise.

The terms “isolated” is not meant to exclude artificial or syntheticmixtures with other compounds or materials, or the presence ofimpurities that do not interfere with the fundamental activity, and thatmay be present, for example, due to incomplete purification, or theaddition of stabilizers.

“Pharmaceutically acceptable” indicates approval by a regulatory agencyof the Federal or a state government or listed in the U.S. Pharmacopeiaor other generally recognized pharmacopeia for use in animals, and moreparticularly in humans.

A “carrier” refers to, for example, a diluent, preservative,antioxidant, solubilizer, emulsifier, adjuvant, excipient, bulkingsubstances, auxilliary agent or vehicle with which an active agent ofthe present invention is administered. Pharmaceutically acceptablecarriers can be sterile liquids, such as water and oils, including thoseof petroleum, animal, vegetable or synthetic origin, such as peanut oil,soybean oil, mineral oil, sesame oil and the like. Water or aqueoussaline solutions and aqueous dextrose and glycerol solutions arepreferably employed as carriers, particularly for injectable solutions.Suitable pharmaceutical carriers are described, for example, in“Remington's Pharmaceutical Sciences” by E. W. Martin.

The term “treat” as used herein refers to any type of treatment thatimparts a benefit to a patient suffering from an injury, includingimprovement in the condition of the patient (e.g., in one or moresymptoms), delay in the progression of the condition, etc.

As used herein, the term “prevent” refers to the prophylactic treatmentof a subject who is at risk of developing a condition and/or sustainingan injury, resulting in a decrease in the probability that the subjectwill develop conditions associated with the injury.

A “therapeutically effective amount” of a compound or a pharmaceuticalcomposition refers to an amount effective to prevent, inhibit, or treata particular injury and/or the symptoms thereof. For example,“therapeutically effective amount” may refer to an amount sufficient tomodulate the pathology associated traumatic brain injury in a patient.

As used herein, the term “subject” refers to an animal, particularly amammal, particularly a human.

A “vector” is a genetic element, such as a plasmid, cosmid, bacmid,phage or virus, to which another genetic sequence or element (either DNAor RNA) may be attached so as to bring about the replication and/orexpression of the attached sequence or element. A vector may be eitherRNA or DNA and may be single or double stranded. A vector may compriseexpression operons or elements such as, without limitation,transcriptional and translational control sequences, such as promoters,enhancers, translational start signals, polyadenylation signals,terminators, and the like, and which facilitate the expression of apolynucleotide or a polypeptide coding sequence in a host cell ororganism.

The following example describes illustrative methods of practicing theinstant invention and is not intended to limit the scope of theinvention in any way.

Example

Huntington disease (HD) is a fatal dominantly inheritedneurodegenerative disorder caused by CAG repeat expansion (˜>36 repeats)within the first exon of the huntingtin gene. Although mutant huntingtin(mHTT) is ubiquitously expressed, the brain shows robust and earlydegeneration. Current RNA interference-based approaches for loweringmHTT expression have been efficacious in mouse models, but basal mutantprotein levels are still detected. To fully mitigate expression from themutant allele, allele specific genome editing can occur via prevalentpromoter-resident single nucleotide polymorphisms (SNP) inheterozygosity with the mutant allele. Here, SNPs are identified thateither cause or destroy PAM motifs critical for CRISPR selective editingof one allele vs. the other in cell from HD patients, and in atransgenic HD model harboring the human allele.

Briefly, SNPs within the promoter or intron 1 with an allelefrequency >10% in the population were identified using the NCBI websiteand the 1000 Genome database. 8 SNPs in which the nucleotide changeeither disrupt and/or generate a PAM motif to allow target specificallyof the mutant HTT allele were identified (Table 1 provides certainexamples). gRNA sequences targeting selected allele specific PAM motifswere designed and cloned into a CRISPR/Cas9 expression cassettecontaining a puromycin selection marker.

Standard human laboratory cell lines (e.g., HEK293, HELA, and NT2),patient fibroblasts, and iPS cells may be genotyped for the selectedSNPs. Different cell lines containing the selected nucleotide variantscan be used to determine allele selectivity and safety of the approach.For HD fibroblasts containing heterozygous SNPs, direct sequencing ofPCR amplified genome sequences containing CAG repeat or SNP linkage bycircularization (SLiC) can be used to identify the linkage between CAGrepeat length and the nucleotide identity (Liu et al. (2008) NatureMethods 5:951-953). After transfection, genomic DNA can be isolated andCRISPR/Cas9 mediated deletions determined by PCR. The effects onhuntingtin expression can be determined by measuring RNA and proteinlevels by Q-PCR and Western blot, respectively. Unintended cleavage ofselected sequences can be determined by using GUIDE-seq method (Tsai etal. (2015) Nature Biotechnol., 33:187-197). Knock in transgenic mice canalso be generated where the promoter, the first exon and/or the firstintronic sequence of the mouse Htt gene are replaced by the orthologoushuman HTT sequence containing the different SNP-nucleotide variants oneach allele. The therapeutic efficacy of the selected sgRNA sequences(e.g., delivered by an AAV viral vector) can be studied in vivo usingcurrent mouse models which exhibit disease phenotypes or the knock inmice.

As explained above, Huntington Disease (HD) is a fatal neurodegenerativedisorder due to polyglutamine (polyQ) disorder caused by triplet CAGrepeat expansion in the huntingtin (HTT) gene. Although huntingtin isubiquitously expressed, the neuropathology of HD is characterized byearly striatal atrophy followed by volume loss in other brain areas(Walker, F. O. (2007) Seminars Neurol., 27:143-150; The Huntington'sDisease Collaborative Research Group (1993) Cell, 72:971-983). There isno cure for HD and treatments are focused on symptom management (Johnsonet al. (2010) Hum. Mol. Genet., 19:R98-R102). Earlier studies usinggenetically modified mouse models showed that HD-like phenotypes can beresolved if mutant huntingtin expression is eliminated, even at advanceddisease stages (Yamamoto et al. (2000) Cell, 101:57-66; Diaz-Hernandezet al. (2005) J. Neurosci., 25:9773-9781), suggesting that therapeuticstrategies focused on eliminating mutant huntingtin expression will behighly beneficial. As examples, knock down strategies using RNAinterference (RNAi) or antisense oligonucleotides, which reduce mutanthuntingtin expression either alone or together with the normalhuntingtin, are beneficial in various mouse models (Harper et al. (2005)Proc. Natl. Acad. Sci., 102:5820-5825; Boudreau et al. (2009) Mol.Ther., 17:1053-1063; Drouet et al. (2009) Ann. Neurol., 65:276-285;Kordasiewicz et al. (2012) Neuron, 74:1031-1044). Other strategies, suchas genome editing with zinc finger nucleases targeted to the CAG-repeatexpansion region, have also been tried (Garriga-Canut et al. (2012)Proc. Natl. Acad. Sci., 109:E3136-3145).

Genome editing with the recently discovered CRISPR/Cas9 systemrepresents an exciting alternative for tackling dominantly inheritedgenetic disorders such as HD (Jinek et al. (2012) Science, 337:816-821;Mali et al. (2013) Science, 339:823-826; Cong et al. (2013) Science,339:819-823). The most recent system advancements involves expressingCas9 along with a guide RNA such as a single guide RNA molecule. Whenco-expressed, gRNAs bind and recruit Cas9 to a specific genomic targetsequence where it mediates a double strand DNA (dsDNA) break, activatingthe dsDNA break repair machinery. Targeted gene deletions bynon-homologous end joining (NHEJ) can be made when a pair of gRNA/Cas9complexes bind in proximity and produce dsDNA breaks (Cong et al. (2013)Science, 339:819-823; Ran et al. (2013) Nat. Protoc., 8:2281-2308; Jineket al. (2013) eLife, 2:e00471).

Given the potency and sequence specificity of the CRISPR/Cas9 targeting,and the fact that huntingtin is an important protein for cell viability(Dragatsis et al. (2000) Nat. Genet., 26:300-306), the use ofCRISPR/Cas9 to direct allele specific genome editing is an attractivealternative to the partial reduction approach using ASOs or RNAimethods. Targeting specificity of the CRISPR/Cas9 complex is regulatedby two different elements, first, the binding complementarity betweenthe targeted genomic DNA sequence (genDNA) and the ˜20 nt-guidingsequence of the gRNA, and secondly, the presence of aprotospacer-adjacent motif (PAM) juxtaposed to the genDNA/gRNAcomplementary region (Jinek et al. (2012) Science, 337:816-821; Cong etal. (2013) Science, 339:819-823; Sternberg et al. (2014) Nature,507:62-67). While previous studies have shown that nucleotide mismatchesat positions 1-10 on the sgRNA-target site interface are not welltolerated for cleavage, sequence context at this region is crucial todetermine which nucleotide positions are more effective to influencecleavage (Jinek et al. (2012) Science, 337:816-821; Ran et al. (2013)Nat. Protoc., 8:2281-2308; Sternberg et al. (2014) Nature, 507:62-67; Fuet al. (2013) Nat. Biotech., 31:822-826; Kuscu et al. (2014) Nat.Biotech., 32:677-683). However, the preservation of an intact PAM motifappears to be critical and genome wide studies searching for Cas9off-target cleavage events demonstrate that mutations on the PAM motifresult on an important reduction of cleavage efficacy (Anders et al.(2014) Nature, 513:569-573; Kleinstiver et al. (2015) Nature,523:481-485; Tsai et al. et al. (2015) Nat. Biotech., 33:187-197;Zetsche et al. (2015) Cell, 163:759-771; Ran et al. (2015) Nature,520:186-191). Therefore, allele specific gene editing can be achieved bytaking advantage of prevalent single nucleotide polymorphisms (SNPs)that either eliminate or create a PAM sequence. In HD, polyglutaminerepeat expansion occurs within exon 1 (Walker, F. O. (2007) SeminarsNeurol., 27:143-150). Because the main regulatory elements for HTTexpression reside within the first 2 Kb 5′ of the transcription startsite (Coles et al. (1998) Hum. Mol. Genet., 7:791-800), SNP-dependentPAMs in heterozygosity with the mutation are natural CRISPR/Cas9 targetsfor allele specific editing. Genomic regions adjacent to HTT exon-1 werescreened to identify SNPs that were prevalent, and were within thecritical position for CRISPR/Cas9- or CRISPR/Cpf1-directed editing.Their utility was tested for allele-specific editing in HD patient celllines and a mouse model expressing full length mutant human HTT.

Methods Prediction of SNP-Dependent PAM Motifs:

SNPs with a prevalence of ≥5% located upstream (6.5 Kb) and downstream(Intron 1) HTT exon1 were obtained from the 1000 Genomes database usingthe NCBI variation viewer website(www.ncbi.nlm.nih.gov/variation/view/?q=HTT&filters=source:dbsnp&assm=GCF_000001405.25).To predict SNP-dependent PAM motifs, SNPs were screened against theconsensus PAM sequences of Streptococcus Pyogenes (SpCas9, NGG or NAG)and Staphylococcus aureus (SaCas9 NNGRRT), or the CRISPR/Cpf1 systems ofAcidaminococcus (AsCpf1, NTTT) and Lachnospiraceae (LbCpf1, heterogenousPAMs). Only those SNPs positioned in a conserved nucleotide PAM positionin which the nucleotide variation disrupted the consensus PAM werepredicted as SNP-dependent PAM motifs.

Cell Culture and Transfection:

Human embryonic kidney (HEK293) cells were maintained in DMEM mediacontaining 10% Fetal Bovine Serum (FBS), 1% L-Glutamine and 1%penicillin/streptomycin at 37° C. with 5% CO₂. Cells were cultured in 24well plates and transfected at 80-90% confluence using Lipofectamine®2000 transfection reagent, according to the manufacturer's protocol.Human HD patient fibroblasts were maintained on MEM media supplementedwith 15% Fetal Bovine Serum (FBS), 1% MEM non-essential amino acids, 1%penicillin/streptomycin and 1% L-Glutamine at 37° C. with 5% CO₂. DNAtransfection was done by electroporation using Invitrogen Neon®transfection reagent using the electroporation conditions (ND31551:1650V, 10 ms, 3 pulses; ND33392: 1450V, 20 ms, 2 pulses), and followingthe guidelines provided by manufacturer.

sgRNA and Cas9 Plasmid Construction:

The plasmid pX330 containing the SpCas9 and sgRNA expression cassetteswas used as a template for further modifications. To determinetransfection efficacy and for selecting positive transfected cells a CMVreporter cassette expressing eGFP/P2A/puromycin fusion protein wascloned downstream of the SpCas9expression cassette. For all sgRNAs theguide complementary sequences were cloned using a single cloning stepwith a pair of partially complementary oligonucleotides. The oligo pairsencoding the genomic complementary guide sequences were annealed andligated into the BbsI cloning site upstream and in frame with theinvariant scaffold of the sgRNA sequence.

Genomic DNA Extraction, SNP Genotyping and Genome Editing Analysis:

Genomic DNA from HD fibroblast and HEK293 cell lines was extracted usingDNeasy® Blood & Tissue kit (Qiagen) according to manufacturer'sinstructions. SNPs were genotyped by direct Sanger sequencing of PCRamplified products containing the SNPs and using the primers listed onTable 2. To determine which nucleotide variation of SNP1 (rs2857935) waslinked to the normal or the mutant allele the genomic sequencecontaining SNP1 and the CAG repeat was amplified by PCR and cloned intoTOPO® plasmids using the TOPO TA cloning kit, and subsequentlytransformed into DH5alpha competent cells. Individual colonies wereanalyzed using Sanger sequencing to determine which nucleotide variantis associated with the normal or mutant allele. Deletions of HTT exon 1were confirmed on genomic DNA samples by PCR, using primers bindingoutside the intervening segment cleaved by the sgRNA/SpCas9 complex pair(Table 2).

TABLE 2 List of primers and oligonucleotides.Oligos to generate guide sequences: Name: Sequence (SEQ ID NOs: 1-20)PosCRPAS1 caccGCTCCAGGCGTCGGCGG NegCRPAS1 aaacCCGCCGACGCCTGGAGCPosCRPAS2 caccGGCGCGGGGCTCAACGGAG NegCRPAS2 aaacCTCCGTTGAGCCCCGCGCCPosCRPAS3 caccGTCTGGGACGCAAGGCGCCG NegCRPAS3 aaacCGGCGCCTTGCGTCCCAGACPosCRPAS4 caccGATGCACGCGGGGTGGGGC NegCRPAS4 aaacGCCCCACCCCGCGTGCATCPosCRPAS5G tcccATTCAGGTTGATGTCCT NegCRPAS5G aaacAGGACATCAACCTGAATPosCRPAS5C tcccATCCCATTCTGAGGTTCTGG NegCRPAS5C aaacCCAGAACCTCAGAATGGGATPosCRPAS6C caccGCAGGCAGAGAGGAGCC NegCRPAS6C aaacGGCTCCTCTCTGCCTGCPosCRPAS6G caccGCCTGGCTAAAGTAGGCTT NegCRPAS6G aaacAAGCCTACTTTAGCCAGGCPosCRi3 caccGCTTTTAGGACGCCICGG NegCRI3 aaacCCGAGGCGTCCTAAAAGC PosCRi4caccGCGGGACACTTCGAGAGG NegCRI4 aaacCCTCTCGAAGTGTCCCGCPrimers to assess cleavage Name: Sequence (SEQ ID NOs: 21-25) Fwd1SNP5′-GAC CAC GCG CAT TCT CT-3′ Fwd4SNP 5′-GGA AAC AGG ACA GAT GAA GGAG-3′Fwd5SNP 5′-CAG CTC AGA CGG AAG TGT ATT T-3′ Fwd6SNP5′-CTC CCA AGA ACT GGG AAC TAA C 3′ Rev3Cleavage5′-ACC ACC GTG ATC ATG AAC TAA A-3′ Primers for genotypingName:Sequence (SEQ ID NOs in parentheses) Fwd1SNP 5′-GAC CAC GCG CAT TCT CT-3′ (21) Rev1SNP 5′-CGG GAC TGC ATG GTA AGG-3′ (26) Seq1SNP 5′-GCT GTC CGG GTG AGT ATG-3′ (27) FwdSNP2 5′-CCC ACC TCT CAC CTT CCT-3′ (28) RevSNP2 5′-CAG CAT GAT TGA CAG CCC TA-3′ (29) Seq2SNP 5′-CCG CGA CAC TTC ACA CA-3′ (30) FwdSNP3 5′-CCG CGA CAC TTC ACA CA-3′ (31) RevSNP3 5′-TGC TGC TGG AAG GAC TTG 3′ (32) Seq3SNP 5′-TAG GGC TGT CAA TCA TGC TG 3′ (33) Fwd4SNP 5′-GGA AAC AGG ACA GAT GAA GGAG-3′ (22) Rev4SNP 5′-GGG AAT TGA GGG CGG TTT AT-3′ (34) Seq4SNP 5′-TTT ACC AGC TCC TGG CTT TC-3′ (35) Fwd5SNP 5′-CAG CTC AGA CGG AAG TGT ATT T-3′ (23) Rev5SNP 5′ GAG CAT GTC CGT GTC CTA ATC-3′ (36) Seq5SNP 5′-TCC CTG GCT AGC ACT TAC TT-3′ (37) Fwd6SNP 5′-CTC CCA AGA ACT GGG AAC TAA C 3′ (24) Rev6SNP 5′-TGT GAT TAG TGC AGC GAG AAG-3′ (38) Seq6SNP 5′-CTG TTT CTC TGC TGT CCT TCT C-3′ (39) Primers for SQ-PCR reactionName: Sequence (SEQ ID NOs: 40-43) FwdHTT  TCGGTGCAGCGGCTCCTC Rev HTT ATGGCGACCCTGGAAAAGCTG FwdActB  TTCGCGGGCGACGATGC RevActB CGTACATGGCTGGGGTGTTG Primers to determine off target indels Name:Sequence (SEQ ID NOs: 44-65) CBFA2T3_Fwd  TCTGTGGTTCAGCCGACTTCCBFA2T3_Rev  ACACAATACCGTGGCAGAGG SLC45A_Fwd  GACCCAAGCTTGCCGTAGTASLC45A_Rev  ACCTGTTCAGCATCGACGAG STT3B_Fwd CCTAACGGACCTGTCGCTTTSTT3B_Rev TGAGGGACGACTTGTGCTTG NAV2_Fwd CCACGAGTGCACACAGTTTG NAV2_RevCTCAAGGACTGCTGGCTCAA NUP210_Fwd  AGCTGCGTGATCTTGACCAA NUP210_Rev GGTGGTTCAGGCTCTTTCCA DNAJC16_Fwd  TCTCATGCACCTCCTCCCAT DNAJC16_Rev TGAGTGCAGCGACATGATCA LEPR_Fwd TGAGATGTGCCTCCCTCAGA LEPR_RevAACTAGTGGCATGCGTTTGC CHRNA2_Fwd  CCTTCTGCATGTGGGGTGAT CHRNA2_Rev TGAGATCATCCCGTCCACCT TRIB1_Fwd TCCCGGGACTTAAAAAGCCG TRIB1_RevACCTGGTCAAATGGCGTCTT SMARCD1_Fwd  TATGGTTTTCCCTCCCGGAC SMARCD1_Rev AGCAGGTGTGTAACTGCCTC COX11_Fwd GTTAGAGGCTGCGGACCTTT COX11_RevGCCGTTTCTTAGGCCAGAGT

RNA Extraction, RT-QPCR and SQ-PCR of HTT Expression Levels:

Total RNA was extracted using TRIzol® (Life Technologies, Grand Island,N.Y., USA) according to the manufacturer's protocol, with the exceptionof 1 μl Glycoblue™ (Life Technologies, Grand Island, N.Y.) in additionto the aqueous phase on the isopropanol precipitation step and a singlewash with cold 70% ethanol. RNA samples were quantified byspectrophotometry and subsequently cDNAs were generated from 1 μg oftotal RNA with random hexamers (TaqMan® RT reagents, AppliedBiosystems). To determine human HTT expression levels in HD fibroblastsand HEK293 cells, TaqMan® probes for human HTT and glyceraldehyde3-phosphate dehydrogenase (GAPDH) mRNAs obtained from Applied Biosystemswere used. For determining human and mouse HTT expression levels inBACHD mice samples TaqMan® Probes for human HTT mRNA, mouse Htt mRNA andmouse beta actin mRNA obtained from Applied Biosystems were used.Relative HTT gene expression was determined using the ddCt method.Allele specific editing was determined by a Semi Quantitative PCRamplification of the CAG repeat within HTT exon 1. RT-PCR experimentswere carried out with cDNAs generated from 1 μg of total RNA and using80 ng for PCR amplification. The RT-exponential phase was determined on25-30 cycles to allow semi-quantitative (SQ) comparison of cDNAsdeveloped from identical reactions with Biolase™ Taq Polymerase (BiolineInc, MA). A SQ-PCR reaction for Actin B (20 cycles) was used as areference gene to determine loading differences between samples. Theprimers are shown in Table 2. Briefly, the high capacity cDNA kit fromApplied Biosystems was used for the Rt-reaction with random hexamers.

Huntingtin Western Blots:

HEK293 cells were transfected with sgRNA/SpCas9 expression cassettes,selected for 2 days with puromycin (3 μM) and expanded until cellsreached confluence. Then, cells were rinsed once with PBS and lysed withpassive lysis buffer (PBL, Promega). Protein concentrations weredetermined using the DC protein assay (BioRad) and 15 μg of proteinloaded on a 3-8% NuPAGE® Tris-Acetate gel (Novex Life Technologies). HDfibroblast cells were electroporated with sgRNA/SpCas9 expressioncassettes, selected for 2 days with puromycin (204) and expanded untilcells reached confluence. Cells were then rinsed with iced-cold PBS,de-attached, pelleted, snap froze, and lysed with SDP lysis buffer (50mM Tris pH8.0, 150 mM NaCl, 1% NP40, 1× complete protease inhibitors,1×phosphatase inhibitors, 100 mM PMSF) followed by incubation on ice for20 minutes with occasional vortexing. Debris was removed bycentrifugation (15 min, 20,000 g 4° C.) and the supernatant retained.Protein concentrations were determined using the DC protein assay(BioRad). Samples (25 μg) were prepared for immunobloting by denaturingthe lysates in LDS sample buffer (Invitrogen) with 2×reducing agent (100mM DTT, Invitrogen) and heating to 70° C. for 10 minutes. Samples wereresolved on a 10% low-bis acrylamide gels (200:1 acrilamide:Bis) withTris-glycine running buffer (25 mM Tris, 190 mM Glycine, 0.1% SDS)containing 10.7 mM Beta mercaptoethanol. Gels were run on ice for 40minutes at 90V through the stack, then at 190 V. Proteins weretransferred overnight at 30V and 4° C. onto polyvinylidene fluoride(PVDF) membranes with NuPage® transfer buffer (Invitrogen: 25 mM Bicine,25 mM Bis-Tris, 1.025 mM EDTA, 5% MeOH, pH7.2). Membranes were blockedwith 5% milk in PBS-T and then blotted with a Human anti-HTT (1:5000,Millipore, CA, USA), or rabbit anti beta-actin (1:40000, Sigma)antibodies followed by horseradish peroxidase-coupled antibodies(1:10,000, mouse; or 1:50,000, Rabbit; Jackson ImmunoResearch, WestGrove, Pa.). Blots were developed with ECL Plus reagents (AmershamPharmacia). HTT reduction was determined by densitometry (n=3independent experiments) of protein levels relative to beta catenin withthe VersaDoc™ Imaging System (Biorad) and Quantity One analysissoftware.

rAAV Vector Design and Production:

For in vivo studies, two different rAAV vectors were generated. Oneexpressed SpCas9 and one the sgRNAs expression cassettes. SpCas9 wasexpressed under the control of a minimal cytomegalovirus immediate-earlygene enhancer/promoter region (CMV promoter) and cloned upstream of aminimal poly A sequence (FBAAV-Cas9). The sgRNA expression cassetteswere moved into an AAV shuttle plasmid containing an eGFP gene under thecontrol of the CMV promoter and upstream of a SV40 pA signal. All rAAVplasmid shuttles have AAV2 inverted terminal repeat sequences. RAAVvectors were produced by standard calcium phosphate transfection methodin HEK293 cells by using the Ad Helper, AAV1 transpackaging and AAVshuttle plasmids. Vector titers were determined by RT PCR and were1×10¹³ vg/ml. Vector purity was also tested by silver stain.

Off-Target Analysis:

Potential off target loci for sgHD guide sequences in the human genomewere determined using the Cas9-Off finder algorithm (Bae et al. (2014)Bioinform., 30:1473-1475). Genomic DNA was extracted from HD humanfibroblasts electroporated with sgHD1 and sgHDi3 and amplicons generatedwith Phusion® polymerase using PCR primers flanking the potential site.Amplicons were subjected to Sanger sequencing to determine mutations inthe cleavage site using specific primers, as well as cloned intoTOPO-cloning system for sequence confirmation using 3-4 colonies/site.

Mouse Studies:

BACHD mice were obtained from Jackson Laboratories (Bar Harbor, Me.).Mice were housed in a temperature-controlled environment on a 12-hourlight/dark cycle. Food and water were provided ad libitum. Mice wereinjected with a combination 1:1 of rAAV2/1-SpCas9 virus andrAAV-hU6sgRNA/eGFP virus. For rAAV injections, mice were anesthetizedwith isofluorane, and 5 μl of rAAV mixture injected unilaterally intothe right striata at 0.2 μl/min (coordinates: +0.86 mm rostral toBregma, +/−1.8 mm lateral to medial, ˜2.5 mm ventral from brainsurface). After 3 weeks, mice were anesthetized with a Ketamine andXylacine mix and perfused with 18 ml of 0.9% cold saline mixed with 2-mlRNAlater® (Ambion) solution. Brains were removed, blocked and cut into1-mm-thick coronal slices. Tissue punches from striata were taken usinga tissue corer (1.4-mm in diameter; Zivic Instruments, Pittsburgh, Pa.).All tissue punches were flash frozen in liquid nitrogen and stored at−80° C. until use.

Statistical Analysis

All statistical analyses were performed using Graph-Pad Prism v5.0software. All data was analyzed using one-way ANOVA followed by aBonferroni's post-hoc, or a Mann Whitney test as indicated. Statisticalsignificance was considered * P<0.05, P<0.01, § P<0.001, #P<0.0001.

Results Screening SNP-Derived PAM Motifs in the HTT Genomic Locus

A goal was to delete the mutant HTT allele using SNP-dependent PAMsflanking HTT exon 1 that when present in heterozygosity would tether theCas9 protein to the mutant, but not the normal allele (FIG. 3A). TheCRISPR/SpCas9 system from Streptococcus pyogenes is the most widelyused, and its PAM sequence (NRG, where N represents any nucleotide, R apurine and the conservation of a guanine) have been characterized (Jineket al. (2012) Science, 337:816-821; Cong et al. (2013) Science,339:819-823). SNPs present at specific PAM positions could generate,remove, or simultaneously do both in a strand specific way (FIG. 3B).Using the NCBI website and the 1000 Genomes database, the upstream (3Kb, Promoter/5′UTR) and downstream (6.5 Kb, Intron 1) genomic sequencesof HTT exon-1 were screened and 47 SNPs with a prevalence of more than5% were identified. Of these, 21 were present within the conserved thirdnucleotide of the PAM sequence of SpCas9 (FIG. 3C, FIG. 5A-5O, FIGS.3D-3J). Overall, the nucleotide variation caused the loss (8 SNPs), gain(8 SNPs), or simultaneously the loss in one DNA strand and the gain onthe opposite strand (5 SNPs, Loss/Gain) (FIG. 1C, FIGS. 3D-3J). FIG. 3Kshows the flanking sequence of the indicated SNPs, the location of thePAMs, and an example of complementary sequence to target the site forcleavage.

Experimental Validation of HTT Promoter SNP-Dependent PAM Motifs

Small guide RNAs (sgRNAs; single guide RNAs) were generated that bindadjacent to PAM sequences representing 5 of the identified SNPs in theupstream ˜6 Kb (SNPs 1, 2, 4, 5, and 6) and to a SNP-dependent PAM nearthe transcription start site (SNP3) (FIGS. 4A, 4B, 6A, and 6B) to testas candidates for CRISPR/Cas9 cleavage in HEK 293 cells. These SNPs havean allele frequency of >10% in the general population, and thenucleotide variations cause the Loss or a Loss/Gain of the PAM motif(Table 3). Common sgRNAs were also designed for the first HTT intron(sgHDi3 and sgHDi4; FIG. 4A and FIGS. 6A and 6B). The sgRNAs were cloneddownstream of the hU6 or hH1 promoter, along with other elements asdepicted (FIG. 2C). HEK 293 cells, which are homozygous for thetargeting SNPs (FIG. 4B) were transfected with SpCas9 and sgRNAexpression plasmids and genomic deletion assessed. DNA products of theanticipated size were amplified in most of the sgRNA/SpCas9 paircomplexes tested (FIG. 4D, 4E, 4F). As expected, HTT remained intact incells expressing SpCas9 or sgHDi3 only, or co-expressing sgHDi3 with asgRNA sequence for which a PAM sequence is absent in the HTT promoter(sgHD5c/i3 and sgHD6g/i3). HTT exon1 cleavage in cells was not detectedtransfected with sgHD5g/i3, in spite of the presence of the PAM. BothsgHD1 and sgHD5g have a 17 nt complementary sequence, yet sgHD1/i3eliminated HTT exon 1 while sgHD5/i3 did not. Interestingly, sgHD1 has 8guanines, 6 cytosines and 1 adenosine whereas sgHD5g has 4 guanines, 3cytosines and 3 adenosines. This is consistent with work showing adirect correlation between the sequence composition of the sgRNAcomplementary region to sgRNA activity, with the most active sequencesenriched for guanine and cytosine and depleted of adenosine(Moreno-Mateos et al. (2015) Nat. Meth., 12:982-988). Sanger sequencingof the small-amplified PCR products confirmed HTT exon1 deletion anddsDNA repair (FIG. 4J).

TABLE 3 List of prevalent SNPs located upstream of human HTT exon1. SNPID, location, nucleotide variation, allele nucleotide frequency, strandand the effect of the nucleotide variation on the PAM sequence areindicated. Allele frequency SNP ID Variant ID Location SNP Reference1000G MAF Strand PAM SNP4 rs35631490 3,071,679 C/G C = 0.8926 G =0.1074 + Loss SNP5 rs61792464 3,073,385 G/C G = 0.8628 C = 0.1372 +Gain/Loss SNP6 rs9996199 3,074,965 C/G C = 0.8425 G = 0.1575 + Gain/LossSNP1 rs2857935 3,075,691 C/G/T C = 0.7710 G = 0.2260 − Loss SNP2rs13122415 3,076,181 C/G C = 0.8918 G = 0.1082 + Loss SNP3 rs131022603,076,405 G/A G = 0.8419 A = 0.1581 + Loss

HTT mRNA and protein levels were reduced in cells following editing, asdetermined by Q-PCR and western blot, respectively (FIGS. 4G, 4H, 4I,and 4K). Reduction of HTT mRNA levels was greater in cells expressingsgRNA/SpCas9 complex pairs that generated small targeted deletions,indicating that HTT exon 1 removal efficacy may be influenced by thedistance between the two dsDNA breaks (compare sgHD1, 2 and 3 versussgHD4 and 6) (FIG. 4G). Also, the results indicate a preference ofSpCas9 for NGG over NAG PAM sequences (compare sgHD1, 2, 3, 4 (NGG) vssgHD6c (NAG)) (FIG. 4G). Interestingly, cells expressing sgHDi3 alone,or in combination with sgHD6g or sgHD5g, also showed reduced HTT mRNAand protein levels albeit not to as great an extent as those where HTTexon 1 was removed. This indicates that elements within the firstintron, disrupted after DNA repair, could affect expression of thenormal HTT allele (FIGS. 4G, 4H, 4I).

FIG. 4L provides a schematic depicting the strategy to delete 1st exonsequence of mutant huntingtin gene using the CRISPR/Cas9 systemtargeting the SNP-derived PAM motifs at positions SNP1, SNP2, SNP3 andSNP6 in combination with the intronic i3 PAM motif. FIG. 4M provides aschematic depicting the strategy to delete 1st exon sequence of mutanthuntingtin gene using the CRISPR/Cas9 system targeting the SNP6 incombination with i3 PAM motif. FIG. 4N provides a schematic depictingthe strategy to delete 1st exon sequence of mutant huntingtin gene usingthe CRISPR/Cas9 system targeting the SNP4, SNP5 derived PAM motifs incombination with i3 PAM motif.

Assessment of Allele Specificity of Editing in HD Human Fibroblasts.

Expression vectors for sgHD1/i3 and SpCas9, or SpCas9 only, weregenerated (FIG. 7A) for screening in HD fibroblast cell lines.Twenty-three lines were screened for SNP heterozygosity using directSanger sequencing of PCR amplified products. Eleven lines wereheterozygous for SNP1, 1 line was heterozygous for SNP2, SNP4 and SNP6,and 2 lines were heterozygous for SNP3 and SNP5 (Table 4). Two lines,ND31551 and ND33392, which are heterozygous for the SNP1 on oppositealleles, were chosen for specificity testing (FIG. 7B, Table 5). PCR ofgenomic DNA showed target cleavage in cells transfected with plasmidsexpressing sgHD1/i3 and SpCas9 relative to those lacking sgRNAs (FIG.7C). Semi-quantitative PCR for the normal and mutant HTT mRNAs showedtarget mRNA knockdown (FIGS. 7D, 7E, 7F), which for ND31551 is thenormal allele, and for ND33392 is the mutant allele. Western blot forprotein confirmed allele specific reduction of the target allele (FIGS.7G, 7H).

TABLE 4 List of Huntington's disease (HD) fibroblast genotypes for thevarious SNPs. HD fibroblast ID, CAG repeat length of the normal andmutant allele, and presence or absence of the SNP heterozygosity areindicated. SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 rs2857935 rs13122415 rs13102260rs35631490 rs61792464 rs9996199 (C > G/T) (C > G) (G > A) (C > G) (C >G) (C > G) HD Fibroblast CAG repeat 0.226 0.1082 0.1581 0.1074 0.13720.1575 GM04723 CAG:72 C/G C G C G C GM04869 CAG:50 C C G C G C GM04767CAG:47 C/G C G C G C GM04867 ND C C G C G C GM04849 ND C C G C G CGM04689 CAG:46 C C G C G C ND29801 CAG:40 C C G C G C ND29970 CAG:40 C CG/A C G/C G/C ND30013 CAG:43 C C G C G C ND30015 CAG:41 C/G C G C G CND30016 CAG:41 C/G C G C G C ND30047 CAG:41 C/G C G C G C ND30259 CAG:38C C G C G C ND30422 CAG:40 C/G C G C G C ND30626 CAG:41 C/G C G C G CND30967 CAG:43 C C G C G C ND31038 CAG:44 C/G C G C G C ND31551 CAG:39C/G C/G G/A C/G G G/C ND31846 CAG:40 C C G C G C ND33392 CAG:57 C/G C GC G C ND33947 CAG:40 C/G C G C G C ND40536 CAG:66 C C G G G C ND40534CAG:46/26 C C G C G C

TABLE 5 Genotypes of 11 HD fibroblast lines heterozygous for SNP1.Fibroblast ID, CAG repeat length, nucleotide variation for normal andmutant allele, allele that contains the PAM motif and family ID of theHD fibroblast line are indicated. Huntingtin Allele HD Fibroblast CAGrepeat SNP Normal Mutant Targeted Family GM04723 CAG:72/17 C/G G CMutant 691 GM04767 CAG:47/18 C/G G C Mutant 691 ND30015 CAG:41/20 C/G GC Mutant NINDS3749 ND30016 CAG:41/21 C/G G C Mutant NINDS3749 ND30047CAG:41/18 C/G G C Mutant NINDS3753 ND30422 CAG:40/18 C/G G C MutantNINDS3751 ND30626 CAG:41/21 C/G G C Mutant NINDS3752 ND31038 CAG:44/19C/G C G Normal NINDS3752 ND31551 CAG:39/18 C/G C G Normal UnknownND33392 CAG:57/17 C/G G C Mutant NINDS4250 ND33947 GAG:40/18 C/G G CMutant Unknown

Assessment of Off-Target Cleavage Sites in HD Human Edited Fibroblasts.

Although truncated sgRNA sequences (˜<20 nt) are reported to have higherselectivity for the on-target site, any sgRNA/Cas9 complex can alsogenerate unwanted dsDNA breaks at off-target sites that resemble theon-target sequence (Fu et al. (2013) Nat. Biotech., 31:822-826;Kleinstiver et al. (2015) Nature, 523:481-485; Hsu et al. (2013) Nat.Biotech., 31:827-832; Cho et al. (2013) Nat. Biotech., 31:230-232). TheCas9-Off finder algorithm was used to predict the number of potentialoff-target sites for the most effective sgRNAs (sgHD1, sgHD2, sgHD3 andsgHDi3), and the UCSC genome browser for mapping their location in thehuman genome (Bae et al. (2014) Bioinform., 30:1473-1475). The screenidentified 416 sites for sgHD1, whereas 40, 21 and 7 off-targets arepredicted for sgHD2, sgHDi3 and sgHD3, respectively (FIG. 8A). Of note,sgHD1 has the shortest complementary sequence (17 nt), which couldexplain its higher frequency for genomic off-targets. Importantly, allguides showed full complementary only to HTT, and more than 90% of theoff-targets have 3 mismatches. As expected, they occur in the promoter,5′UTR, exons, introns, 3′ UTR, and intergenic regions. The highestnumber was predicted within introns (FIG. 8B). HD fibroblasts wereelectroporated with vectors expressing SpCas9 and sgHD1/i3, along with ashort ODN sequence for mapping off-target dsDNA breaks (Tsai et al.(2015) Nat. Biotech., 33:187-197). As expected, the ODN was incorporatedwithin the HTT gene locus (FIG. 8C) but it was not detected in any ofthe 11 top off-target sites tested (FIG. 8D).

Allele-Specific Editing In Vivo.

BacHD mice are transgenic for a modified human HD allele (Gray et al.(2008) J. Neurosci., 28:6182-6195), which fortuitously contains SNPs 1,2 and 3. These mice were used to first evaluate the efficacy of mutantHTT editing in vivo at the genomic level. For this, recombinant AAVs(rAAVs) expressing either SpCas9 (rAAV.SpCas9) or the sgRNAs(rAAV.sgHD1/i3) were generated, which effectively delete human HTT exon1 in vitro (FIG. 9A, 9D). Mice were injected on the right hemispherewith rAAV.SpCas9 plus rAAV.sgHD1B/i3. The left hemisphere was used as acontrol and left uninjected. Brains were harvested 3 weeks later andgenomic DNA isolated. PCR amplification of genomic DNA demonstratescleavage in the setting of Cas9 and sgRNA expressing AAVs only (FIG.9B). Accordingly, HTT mRNA levels reduced on the right, but not the lefthemisphere, in concordance with DNA cleavage (FIG. 9C). Interestingly,mouse Httm RNA levels were also reduced on the injected hemisphere,although to a lesser degree than the human HTT allele. Several bindingsites for sgHD1 and sgHDi3 were identified within the mouse Htt locus.Three binding sites were identified for sgHD1, all within exon 1 andcontaining 5 mismatches. In contrast, a single binding site with 2mismatches within the first intron was predicted for sgHDi3 (FIG. 9E).Indels within the intron caused by sgHDi3 may disrupt transcriptionfactor binding sites, and similar to HEK293 cells expressing sgHDi3alone (FIG. 4G), reduce mouse HTT expression.

Other Cas9 Systems for Silencing the HTT Allele.

It was then screened which of the 47 SNPs flanking HTT exon1 werecontained within their conserved PAM nucleotide positions. EngineeredSpCas9 variants from Streptococcus Pyogenes with altered PAMspecificities have been generated (SpCas9 VQR, SpCas9 EQR, and SpCas9VRER) (Kleinstiver et al. (2015) Nature, 523:481-485). The SpCas9 VQRvariant strongly recognizes sequences bearing the NGAN PAM and withlower efficiency those sites with a NGNG motif. SpCas9_EQR is morespecific for an NGAG PAM. In contrast, SpCas9_VRER has a strongselectivity for a NGCG PAM sequence with no cleavage activity when thisis varied. For SpCas9 VQR, the SNP could be positioned at the 2nd or the3rd nucleotide of the NGAN PAM, as well as at the 2nd and 4th nucleotideof the NGNG PAM sequence. In contrast, because of the selectivity of theSpCas9 EQR for NGAG and SpCas9 VRER for NGCG sequences, the SNP could bepermitted at any position of their PAM (FIG. 5A-5O, FIGS. 3D-3J). Thediscovery of SaCas9 from Staphylococcus aureus has extended the numberof CRISPR/Cas9 systems, with the advantage that a SaCas9-encodingtransgene can be easily package into AAV viral vectors (Ran et al.(2015) Nature, 520:186-191). SaCas9 primarily recognizes a NNGRRT PAM,although dsDNA breaks are also observed at DNA targets adjacent to NNGRRmotifs. For SaCas9 only those SNPs positioned at the 3rd nucleotide ofthe PAM would allow for allele specificity (FIG. 5A-5O, FIGS. 3D-3J). Anew Class 2 CRISPR system was recently identified that contains Cpf1 aseffector protein to mediate dsDNA breaks (Zetsche et al. (2015) Cell,163:759-771). Unlike Cas9 that recognizes a G-rich PAM motif, the Cpf1PAM motif is T-rich. Currently, 16 Cpf1-family proteins have beencharacterized, but only the Cpf1 proteins from Acidaminococcus (AsCpf1)and Lachnospiraceae (LbCpf1) have shown robust DNA interference activitywhen expressed in mammalian cells. AsCpf1 has strong selectivity for aTTTN PAM and does not recognize any sequence variants. Therefore, SNPpresents at any position of the TTTN PAM could disrupt AsCpf1recognition. In contrast, LbCpf1 recognizes multiple T-rich PAMs, albeitwith different cleavage activity. Thus, for LbCpf1, only those SNPswhere the variant nucleotide did not generate any other PAM that couldbe recognized above LbCpf1 cleavage threshold activity could beconsidered for allele discrimination (Zetsche et al. (2015) Cell,163:759-771) (FIGS. 5A-5O, FIGS. 3D-3J).

Overall, 36 SNPs located within the specific PAM positions describedabove were identified. Again, instances where the nucleotide variationcaused the loss (12 SNPs), gain (11 SNPs), or a simultaneous loss in oneDNA strand and a gain on the opposite strand (13 SNPs) were identified(FIGS. 5A-5O, FIGS. 3D-3J). Of special interests are the SNPs thatgenerate a Loss/Gain, since CRISPR complexes could be designed for anyof the two possible nucleotides linked to the mutant allele. Of note,instances were found where the same Cas9 protein could target eachnucleotide variation using a different sgRNA sequence, or alternatively,a different CRISPR effector protein could be used to target eachnucleotide variant. Two interesting observations also arose from thescreen. One, in the rs113331544 SNP, for which the minor allele containsa six-nucleotide insertion, the same PAM sequence is present on bothalleles, but a different sgRNA sequence could be designed to tetherSpCas9 to the mutant allele depending on the nucleotide variation. Two,for the rs28393280 and the rs28583447 SNPs, the nucleotide variationcauses the gain of 2 PAM motifs on the same allele, one on the positiveand the other on the negative DNA strand. Those SNPs could beappropriate for targeting with a nickase effector protein, which wouldefficiently generate on-target dsDNA breaks without detectable damage atpotential off-target sites (Ran et al. (2013) Cell, 154:1380-1389).

Currently, reduction of HTT mRNA levels with RNAi and ASOs are theleading therapeutic options for HD (Kordasiewicz et al. (2012) Neuron,74:1031-1044; McBride et al. (2011) Mol. Ther., 19:2152-2162). However,it is unknown whether these treatments will be beneficial in HDpatients, since the mutant protein is not completely eliminated.Additionally, the normal allele is reduced relative to normal levels asa consequence of the non-allele specific gene silencing approach.

Targeted gene deletions can be generated when two sgRNA/Cas9 complexescause dsDNA breaks followed by DNA repair (Cong et al. (2013) Science,339:819-823; Jinek et al. (2013) eLife, 2:e00471). Given the potency ofCRISPR/Cas9 and the high likelihood of cleaving both HTT alleles, therole of HTT protein on important cellular functions, and the fact that acomplete loss of the huntingtin gene in adult mice causes progressiveneurodegeneration (Dragatsis et al. (2000) Nat. Genet., 26:300-306),allele specificity for editing is imperative. Earlier work demonstratedthat Cas9 causes dsDNA breaks when mismatches are present between theguide and the targeted sequence, but only if a PAM motif is near thetarget sequence (Fu et al. (2013) Nat. Biotech., 31:822-826; Hsu et al.(2013) Nat. Biotech., 31:827-832). Genome wide studies and in vitrolibrary screens have provided information regarding the conservation foreach nucleotide within a PAM sequence for several of the available Cas9proteins (Kleinstiver et al. (2015) Nature, 523:481-485; Tsai et al.(2015) Nat. Biotech., 33:187-197; Zetsche et al. (2015) Cell,163:759-771; Ran et al. (2015) Nature, 520:186-191). Cas9 PAMrecognition could be disrupted on a single allele if aSNP located atthese conserved nucleotides were present in heterozygosity. Thus, singleallele targeted deletions could be generated to mitigate the expressionof the mutant, but not the normal allele.

Guide RNAs were designed that bind and tether SpCas9 to six prevalentSNPs located 5′ of HTT exon1, which in combination with a guide bindingwithin the first HTT intron effectively eliminate expression of the HTTprotein. The distance between upstream and downstream guides influencedediting efficacy, as well as confirmed the SpCas9 preference in HD celllines. The studies also indicate that intronic transcription bindingsites may effect HTT gene expression, since indels generated by SpCas9within the HTT intron reduced gene expression. This is important whendesigning intronic guide sequences, since expression of the normalallele could also be affected. The allele specificity of the instantapproach was demonstrated using human fibroblast cell lines for whichthese SNPs are present in heterozygosity. HTT exon 1 excision wasobserved only on the alleles where the nucleotide variation did notdisrupt the PAM motif.

Interestingly, SNP1 (rs2857935) has a prevalence of 22% among the humanpopulation. In the HD fibroblast lines, 9 out of 11 were heterozygousfor the SNP and the PAM was linked to the mutant allele. This raises theexciting possibility that this SNP is in linkage disequilibrium with themutant allele in the general HD population.

The importance of on-target selectivity is crucial when usinggene-editing approaches. In the instant strategy truncated sgRNA guideswere used, which have been shown to minimize unintended dsDNA breaks (Fuet al. (2014) Nat. Biotech., 32:279-284). Potential off-targets from theguides were screened for using an in silico approach, and most of theoff-target binding sites contained 3 mismatches within intronic regions.Notably, additional tools with significant on-target selectivity such asthe High fidelity Cas9 proteins and the Cas9 nickases can be used in theinstant methods (Ran et al. (2013) Cell, 154:1380-1389; Kleinstiver etal. (2016) Nature, 529:490-495; Slaymaker et al. (2016) Science,351:84-88).

The approach was also demonstrated in vivo using an HD mouse model. rAAVdelivery of the sgRNA/SpCas9 complexes reduced human mutant HTTexpression to 40% in treated hemispheres, a level of reduction known toprovide benefit by RNAi or ASOs (Harper et al. (2005) Proc. Natl. Acad.Sci., 102:5820-5825; Boudreau et al. (2009) Mol. Ther., 17:1053-1063;Kordasiewicz et al. (2012) Neuron, 74:1031-1044). Notably, Cas9 and/orthe sgRNAs may be transiently expressed in the instant methods (Hendelet al. (2015) Nat. Biotech., 33:985-989; Randar et al. (2015) Proc.Natl. Acad. Sci., 112:E7110-7117).

Thus, a strategy for allele specific genome-editing of mutant HTT basedon CRISPR/Cas9 technology has been developed that takes advantage ofhighly prevalent SNPs at the HTT locus for guiding mutant allelespecific cleavage.

A number of publications and patent documents are cited throughout theforegoing specification in order to describe the state of the art towhich this invention pertains. The entire disclosure of each of thesecitations is incorporated by reference herein.

While certain of the preferred embodiments of the present invention havebeen described and specifically exemplified above, it is not intendedthat the invention be limited to such embodiments. Various modificationsmay be made thereto without departing from the scope and spirit of thepresent invention, as set forth in the following claims.

What is claimed is:
 1. A method for inhibiting, treating, and/or preventing a polyglutamine disorder in a subject in need thereof, said method comprising reducing the expression of a mutant protein encoded by an allele of a gene associated with the polyglutamine disorder in said subject, wherein said polyglutamine disorder is characterized by an abnormally high number of cytosine-adenine-guanine (CAG) repeats resulting in an extended polyglutamine tract in the encoded for mutant protein, and wherein said method comprising administering to the subject a nucleic acid molecule encoding Cas9 and at least one guide RNA.
 2. A method for reducing the expression of a mutant protein encoded by an allele of a gene associated with a polyglutamine disorder in a cell, said method comprising delivering to the cell a nucleic acid molecule encoding Cas9 and at least one guide RNA, wherein said polyglutamine disorder is characterized by an abnormally high number of cytosine-adenine-guanine (CAG) repeats resulting in an extended polyglutamine tract in the encoded for mutant protein.
 3. The method of claim 1, wherein said polyglutamine disorder is Huntington's disorder and said gene is the huntingtin (HTT) gene.
 4. The method of claim 1, wherein said method comprises administering to the subject a nucleic acid molecule encoding Cas9, at least one guide RNA, and, optionally at least one donor DNA.
 5. The method of claim 1, wherein said guide RNA are administered as a nucleic acid molecule encoding said guide RNA.
 6. The method of claim 5, wherein said nucleic acid molecules are administered in an expression vector.
 7. The method of claim 6, wherein said expression vector is a viral vector.
 8. The method of claim 1, wherein at least one guide RNA targets a sequence adjacent to a PAM present on only one allele of the gene.
 9. The method of claim 8, wherein said PAM is present only on the mutant allele.
 10. The method of claim 1, wherein two guide RNAs are administered.
 11. The method of claim 10, wherein at least one of the guide RNA targets a sequence adjacent to a PAM present on only one allele of the gene.
 12. The method of claim 10, wherein a first guide RNA targets a sequence within the promoter or 5′ untranslated region of the gene and a second guide RNA targets a sequence within the first intron of the gene.
 13. The method of claim 10, wherein the first guide RNA comprises sgHD1 and the second guide RNA comprises sgHDi3.
 14. An isolated guide RNA, wherein said guide RNA targets a sequence adjacent to a PAM present on only one allele of a gene associated with a polyglutamine disorder.
 15. A nucleic acid molecule encoding at least one of the guide RNA of claim
 14. 16. A vector comprising the nucleic acid molecule of claim
 15. 17. The vector of claim 16, which is a viral vector.
 18. The vector of claim 16, further comprising a nucleic acid molecule encoding Cas9.
 19. A composition comprising at least one nucleic acid molecule of claim 15 and a carrier.
 20. A composition comprising at least one guide RNA of claim 14 and a carrier. 